Development/GDB

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Description Content
module load devel/gdb
Availability bwUniCluster | BwForCluster_Chemistry
License GPL
Citing n/a
Links Homepage | Documentation | Wiki | Mailinglists
Graphical Interface No
Included modules icc | icpc | ifort | idb


Introduction

The GNU Debugger (GDB) is a standard debugger for serial programs although it can be used for parallel and even distributed programs with few processes too. The Intel Debugger (IDB) uses the same commands for basic debugging as GDB and hence can be used instead of GDB just by substituting idbc for gdb.

Versions and Availability

A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the

Cluster Information System CIS

{{#widget:Iframe |url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/devel/gdb |width=99% |height=120 }} On the command line interface of any bwHPC cluster you'll get a list of available versions by using the command 'module avail devel/gdb'. 

$ : bwUniCluster
$ module avail devel/gdb
------------------------ /opt/bwhpc/common/modulefiles -------------------------
devel/gdb/7.7

Attention!
The default Linux GDB may be a different version. Check the default version by: 'gdb --version' without loaded GDB-module. 

$ module clear                             # clear all loaded modules
Are you sure you want to clear all loaded modules!? [n] y
$ gdb --version                            # this is the default version
GNU gdb (GDB) Red Hat Enterprise Linux (7.2-83.el6)
[...]
$ module avail devel/gdb                   # available GDB-module
------------------------ /opt/bwhpc/common/modulefiles -------------------------
devel/gdb/7.7

It is not recommended (or impossible) the debug MPI-based binaries with GDB. You can't attach to MPI'ed jobs, too.

Loading

It is possible to choose between several versions of GDB. By default both programs are installed. You can check the version which is currently used with: 

$ gdb --version
$ gcc --version


To use a different version of GCC or GDB, you have to load it through the module system. For example you need GDB 7.7 or higher for GCC version 4.8 and above. In this case load the devel/gdb module.
How to load the desired version (e.g. GDB version 7.7): 

$ module load devel/gdb/7.7


If you want to use IDB load the Intel compiler module: 

$ module load compiler/intel


Documentation

For online documentation see the links section in the summary table at the top of this page. For local documentation consult the man page. 

$ man gdb

or 

$ man idb


Basic commands

The code you want to debug should be compiled with the -g option. If the optimization flag is not set, the GCC will still do some basic optimization. Therefore, it is recommended to turn off the optmization explicitly with the -O0 parameter for debugging. To start a debug session for a program execute GDB with the program path as parameter: 

$ gdb ./example

Inside GDB is a prompt where you can enter commands. Important commands are listed below.

Command Description
help cmd Show help for command cmd.
break func Set a breakpoint at function func.
run Start program.
next Go to next program line. Do not enter functions.
step Go to next program line. Enter functions.
list Show the surrounding source code of the currently processed line.
print expr Print the value of the expression expr.
display expr Display the value of the expression expr every time the program stops.
watch expr Stop when value of the expression expr changes.
continue Continue execution until a breakpoint or a watchpoint appears.
backtrace Print a list of functions that are currently active.
quit Exit GDB.

Example: We debug the following program called bug.c which crashes on execution. 

#include <stdio.h>

int global = 0;

void begin() {
    global = 1;
}

void loop() {
    int v[2];
    int i, k;

    for(i = 0; i < 8; i++) {
        k = i/2*2;	/* should have been k = i/(2*2); */
        v[k] = i;
    }
}

void end() {
    global = 2;
}

int main() {
    begin();
    loop();
    end();

    return 0;
}

Sample GDB session: 

$ gcc -g bug.c -o bug
$ gdb ./bug
GNU gdb (GDB) Red Hat Enterprise Linux (7.2-60.el6_4.1)
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /pfs/data2/home/xx/xxx/xxxx/bug...done.
(gdb) break main
Breakpoint 1 at 0x4005b2: file bug.c, line 26.
(gdb) run
Starting program: /pfs/data2/home/xx/xxx/xxxx/bug

Breakpoint 1, main () at bug.c:26
26              begin();
Missing separate debuginfos, use: debuginfo-install glibc-2.12-1.132.el6.x86_64 libgcc-4.4.7-4.el6.x86_64
(gdb) next
27              loop();
(gdb) next

Program received signal SIGSEGV, Segmentation fault.
0x0000000000000005 in ?? ()
(gdb) # now we know that the bug is in loop(). start again.
(gdb) run
The program being debugged has been started already.
Start it from the beginning? (y or n) y
Starting program: /pfs/data2/home/xx/xxx/xxxx/bug

Breakpoint 1, main () at bug.c:26
26              begin();
(gdb) next
27              loop();
(gdb) step
loop () at bug.c:13
13              for(i = 0; i < 8; i++)
(gdb) next
15                      k = i/2*2;
(gdb) next
16                      v[k] = i;
(gdb) # maybe k gets too big?
(gdb) watch (k >= 2)
Hardware watchpoint 2: (k >= 2)
(gdb) continue
Continuing.
Hardware watchpoint 2: (k >= 2)

Old value = 0
New value = 1
loop () at bug.c:16
16                      v[k] = i;
(gdb) # k is too big
(gdb) print k
$1 = 2
(gdb) print i
$2 = 2
(gdb) quit


Core dumps

When the program crashes, a log file (called core dump) can be created which contains the state of the program when it crashed. This is turned off by default because these core dumps can get quite large. If you want to turn it on you have to change your ulimits, for example: 

$ ulimit -c unlimited

Every time your program crashes a new file called core.xxx (where xxx is a number) will be created in the directory from which you started the executable. You can call gdb to examine your core dump using the following command (assuming your program is called ex): 

$ gdb ./ex core.xxx

Now you can print a backtrace to check in which function the error happened and what values the parameters had. Additionally you can examine the values of your variables to reproduce the error.

Multithreaded debugging

GDB can also be useful for multithreaded applications for example when OpenMP was used. By going through each thread separately you can better see what is really going on and you can check the computation step by step. The following commands are useful for multithreaded debugging:

Command Description
info threads Shows the status of all existing threads.
thread num Switches to the thread with the number num

Example: We debug the following program called thread_bug.c which crashes on execution. 

#include <stdio.h>
#include <pthread.h>

pthread_t thread;

void* thread3 (void* d)
{
    int w[2];
    int c, l;

    for(c = 0; c < 8; c++) {
        l = c/2*2;	/* should have been l = c/(2*2); */
        w[l] = c;
    }

    return NULL;
}

void* thread2 (void* d)
{
    int v[2];
    int i, k;

    for(i = 0; i < 8; i++) {
        sleep(4);
        k = i/(2*2);    /* should have been k = i/(2*2); */
        v[k] = i;
    }

    return NULL;
}

int main (){

    pthread_create (&thread, NULL, thread2, NULL);
    pthread_create (&thread, NULL, thread3, NULL);
  
    //Thread 1
    int count1 = 0;

    while(count1 < 4000){
      printf("Thread 1: %d\n", count1++);
    }

    pthread_join(thread, NULL);
    return 0;
}

Sample GDB thread session: 

$ gcc -g thread_bug.c -o thread_bug -lpthread
$ gdb ./thread_bug
[...]
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /pfs/data2/home/xx/xxx/xxxx/bug...done.
(gdb) break thread3
Breakpoint 1 at 0x40060c: file thread_bug.c, line 11.
(gdb) break thread2
Breakpoint 2 at 0x400650: file thread_bug.c, line 24.
(gdb) break main
Breakpoint 3 at 0x40069e: file thread_bug.c, line 35.
(gdb) run
Starting program: /tank/home/doros/.t/thread_bug 
[Thread debugging using libthread_db enabled]

Breakpoint 3, main () at thread_bug.c:35
35	  pthread_create (&thread, NULL, thread2, NULL);
Missing separate debuginfos, use: debuginfo-install glibc-2.12-1.132.el6.x86_64
(gdb) info threads
* 1 Thread 0x7ffff7fe5700 (LWP 28260)  main () at thread_bug.c:35
(gdb) next
[New Thread 0x7ffff7fe3700 (LWP 28303)]
36	  pthread_create (&thread, NULL, thread3, NULL);
(gdb) info threads
  2 Thread 0x7ffff7fe3700 (LWP 28303)  thread2 (d=0x0) at thread_bug.c:24
* 1 Thread 0x7ffff7fe5700 (LWP 28260)  main () at thread_bug.c:36
(gdb) next
[Switching to Thread 0x7ffff7fe3700 (LWP 28303)]

Breakpoint 2, thread2 (d=0x0) at thread_bug.c:24
24	    for(i = 0; i < 8; i++) {
(gdb) next
25		sleep(4);
(gdb) next
[New Thread 0x7ffff77e2700 (LWP 28344)]
[Switching to Thread 0x7ffff77e2700 (LWP 28344)]

Breakpoint 1, thread3 (d=0x0) at thread_bug.c:11
11	    for(c = 0; c < 8; c++) {
(gdb) info threads
* 3 Thread 0x7ffff77e2700 (LWP 28344)  thread3 (d=0x0) at thread_bug.c:11
  2 Thread 0x7ffff7fe3700 (LWP 28303)  0x000000362f8accdd in nanosleep () from /lib64/libc.so.6
  1 Thread 0x7ffff7fe5700 (LWP 28260)  0x000000362f8725db in _IO_new_file_overflow () from /lib64/libc.so.6
(gdb) thread 2
[Switching to thread 2 (Thread 0x7ffff7fe3700 (LWP 28303))]#0  0x000000362f8accdd in nanosleep () from /lib64/libc.so.6
(gdb) next
Single stepping until exit from function nanosleep,
which has no line number information.
[Switching to Thread 0x7ffff77e2700 (LWP 28344)]

Breakpoint 1, thread3 (d=0x0) at thread_bug.c:11
11	    for(c = 0; c < 8; c++) {
(gdb) thread 2
[Switching to thread 2 (Thread 0x7ffff7fe3700 (LWP 28303))]#0  0x000000362f8acce9 in nanosleep () from /lib64/libc.so.6
(gdb) next
Single stepping until exit from function nanosleep,
which has no line number information.
0x000000362f8acb50 in sleep () from /lib64/libc.so.6
(gdb) info threads
  3 Thread 0x7ffff77e2700 (LWP 28344)  thread3 (d=0x0) at thread_bug.c:11
* 2 Thread 0x7ffff7fe3700 (LWP 28303)  0x000000362f8acb50 in sleep () from /lib64/libc.so.6
  1 Thread 0x7ffff7fe5700 (LWP 28260)  0x000000362f8476f0 in vfprintf () from /lib64/libc.so.6
(gdb) thread 3
[Switching to thread 3 (Thread 0x7ffff77e2700 (LWP 28344))]#0  thread3 (d=0x0) at thread_bug.c:11
11	    for(c = 0; c < 8; c++) {
(gdb) next
12	        l = c/2*2;	/* should have been l = c/(2*2); */
(gdb) watch (k >= 2)
No symbol "k" in current context.
(gdb) watch (l >= 2)
Hardware watchpoint 4: (l >= 2)
(gdb) continue
Continuing.
Thread 1: 0
Thread 1: 1
Thread 1: 2
Thread 1: 3
Thread 1: 4
[...]
Hardware watchpoint 4: (l >= 2)

Old value = 0
New value = 1
thread3 (d=0x0) at thread_bug.c:13
13	        w[l] = c;
(gdb) print l
$1 = 2
(gdb) print c
$2 = 2
(gdb) quit

Disassembling

Command Description
info functions Shows names and data types of all defined functions.
info line "function" Map source lines to memory adresses (and back).
disassemble function Disassembles "function" (or a function fragment).
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